[English] 日本語
Yorodumi
- EMDB-18398: CryoEM structure of UVSSA(VHS)-CSA-DDB1-DDA1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-18398
TitleCryoEM structure of UVSSA(VHS)-CSA-DDB1-DDA1
Map dataComposite map of UVSSA(VHS)-CSA-DDB1-DDA1
Sample
  • Complex: Ternary complex of UVSSA(VHS)-CSA-DDB1-DDA1
    • Protein or peptide: DNA excision repair protein ERCC-8
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: DET1- and DDB1-associated protein 1
    • Protein or peptide: UV-stimulated scaffold protein A
KeywordsUbiquitin ligase / DNA repair / LIGASE
Function / homology
Function and homology information


regulation of transcription-coupled nucleotide-excision repair / nucleotide-excision repair complex / single strand break repair / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / double-strand break repair via classical nonhomologous end joining / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont ...regulation of transcription-coupled nucleotide-excision repair / nucleotide-excision repair complex / single strand break repair / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / double-strand break repair via classical nonhomologous end joining / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / Cul4A-RING E3 ubiquitin ligase complex / WD40-repeat domain binding / ubiquitin ligase complex scaffold activity / Cul4B-RING E3 ubiquitin ligase complex / negative regulation of reproductive process / negative regulation of developmental process / RNA polymerase II complex binding / cullin family protein binding / viral release from host cell / response to X-ray / positive regulation of DNA repair / ectopic germ cell programmed cell death / proteasomal protein catabolic process / protein autoubiquitination / transcription-coupled nucleotide-excision repair / positive regulation of viral genome replication / response to UV / positive regulation of gluconeogenesis / regulation of circadian rhythm / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / Wnt signaling pathway / Formation of Incision Complex in GG-NER / nuclear matrix / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / protein polyubiquitination / positive regulation of protein catabolic process / rhythmic process / chromosome / cellular response to UV / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / protein-macromolecule adaptor activity / site of double-strand break / chromosome, telomeric region / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / response to oxidative stress / damaged DNA binding / protein ubiquitination / DNA repair / DNA damage response / negative regulation of apoptotic process / protein-containing complex binding / nucleolus / apoptotic process / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
UV-stimulated scaffold protein A / : / : / Uncharacterized conserved protein (DUF2043) / UVSSA N-terminal domain / DET1- and DDB1-associated protein 1, N-terminal / DET1- and DDB1-associated protein 1 / DNA excision repair protein Rad28/ERCC8/Ckn1/ATCSA-1 / Det1 complexing ubiquitin ligase / ENTH/VHS ...UV-stimulated scaffold protein A / : / : / Uncharacterized conserved protein (DUF2043) / UVSSA N-terminal domain / DET1- and DDB1-associated protein 1, N-terminal / DET1- and DDB1-associated protein 1 / DNA excision repair protein Rad28/ERCC8/Ckn1/ATCSA-1 / Det1 complexing ubiquitin ligase / ENTH/VHS / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / : / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / CPSF A subunit region / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
DNA excision repair protein ERCC-8 / DNA damage-binding protein 1 / UV-stimulated scaffold protein A / DET1- and DDB1-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLee S-H / Sixma TK
Funding support Netherlands, European Union, 2 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)TOP 714.017.003 Netherlands
European Molecular Biology Organization (EMBO)ALTF 1159-2019European Union
CitationJournal: To Be Published
Title: CryoEM structure of UVSSA(VHS)-CSA-DDB1-DDA1
Authors: Lee S-H / Sixma TK
History
DepositionSep 6, 2023-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateAug 14, 2024-
Current statusAug 14, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_18398.png

Downloads & links

-
Map

FileDownload / File: emd_18398.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of UVSSA(VHS)-CSA-DDB1-DDA1
Voxel sizeX=Y=Z: 1.057 Å
Density
Contour LevelBy AUTHOR: 0.828
Minimum - Maximum-1.8985326 - 85.661789999999996
Average (Standard dev.)0.0013382172 (±0.94812536)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 338.24 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Ternary complex of UVSSA(VHS)-CSA-DDB1-DDA1

EntireName: Ternary complex of UVSSA(VHS)-CSA-DDB1-DDA1
Components
  • Complex: Ternary complex of UVSSA(VHS)-CSA-DDB1-DDA1
    • Protein or peptide: DNA excision repair protein ERCC-8
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: DET1- and DDB1-associated protein 1
    • Protein or peptide: UV-stimulated scaffold protein A

-
Supramolecule #1: Ternary complex of UVSSA(VHS)-CSA-DDB1-DDA1

SupramoleculeName: Ternary complex of UVSSA(VHS)-CSA-DDB1-DDA1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#4, #1
Details: Ternary complex of ubiquitinated UVSSA-USP7-CSA-DDB1-DDA1. USP7 is invisible in the cryoEM map.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 210 KDa

-
Macromolecule #1: UV-stimulated scaffold protein A

MacromoleculeName: UV-stimulated scaffold protein A / type: protein_or_peptide / ID: 1 / Details: The construct contains an N-terminal His tag. / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 82.923164 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAHHHHHHSA ALEVLFQGPG MDQKLSKLVE ELTTSGEPRL NPEKMKELKK ICKSSEEQLS RAYRLLIAQL TQEHAEIRLS AFQIVEELF VRSHQFRMLV VSNFQEFLEL TLGTDPAQPL PPPREAAQRL RQATTRAVEG WNEKFGEAYK KLALGYHFLR H NKKVDFQD ...String:
MAHHHHHHSA ALEVLFQGPG MDQKLSKLVE ELTTSGEPRL NPEKMKELKK ICKSSEEQLS RAYRLLIAQL TQEHAEIRLS AFQIVEELF VRSHQFRMLV VSNFQEFLEL TLGTDPAQPL PPPREAAQRL RQATTRAVEG WNEKFGEAYK KLALGYHFLR H NKKVDFQD TNARSLAERK REEEKQKHLD KIYQERASQA EREMQEMSGE IESCLTEVES CFRLLVPFDF DPNPETESLG MA SGMSDAL RSSCAGQVGP CRSGTPDPRD GEQPCCSRDL PASAGHPRAG GGAQPSQTAT GDPSDEDEDS DLEEFVRSHG LGS HKYTLD VELCSEGLKV QENEDNLALI HAARDTLKLI RNKFLPAVCS WIQRFTRVGT HGGCLKRAID LKAELELVLR KYKE LDIEP EGGERRRTEA LGDAEEDEDD EDFVEVPEKE GYEPHIPDHL RPEYGLEAAP EKDTVVRCLR TRTRMDEEVS DPTSA AAQL RQLRDHLPPP SSASPSRALP EPQEAQKLAA ERARAPVVPY GVDLHYWGQE LPTAGKIVKS DSQHRFWKPS EVEEEV VNA DISEMLRSRH ITFAGKFEPV QHWCRAPRPD GRLCERQDRL KCPFHGKIVP RDDEGRPLDP EDRAREQRRQ LQKQERP EW QDPELMRDVE AATGQDLGSS RYSGKGRGKK RRYPSLTNLK AQADTARARI GRKVFAKAAV RRVVAAMNRM DQKKHEKF S NQFNYALN

UniProtKB: UV-stimulated scaffold protein A

-
Macromolecule #2: DNA excision repair protein ERCC-8

MacromoleculeName: DNA excision repair protein ERCC-8 / type: protein_or_peptide / ID: 2
Details: The construct contains a Strep tag II at the C-terminus
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.465613 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MLGFLSARQT GLEDPLRLRR AESTRRVLGL ELNKDRDVER IHGGGINTLD IEPVEGRYML SGGSDGVIVL YDLENSSRQS YYTCKAVCS IGRDHPDVHR YSVETVQWYP HDTGMFTSSS FDKTLKVWDT NTLQTADVFN FEETVYSHHM SPVSTKHCLV A VGTRGPKV ...String:
MLGFLSARQT GLEDPLRLRR AESTRRVLGL ELNKDRDVER IHGGGINTLD IEPVEGRYML SGGSDGVIVL YDLENSSRQS YYTCKAVCS IGRDHPDVHR YSVETVQWYP HDTGMFTSSS FDKTLKVWDT NTLQTADVFN FEETVYSHHM SPVSTKHCLV A VGTRGPKV QLCDLKSGSC SHILQGHRQE ILAVSWSPRY DYILATASAD SRVKLWDVRR ASGCLITLDQ HNGKKSQAVE SA NTAHNGK VNGLCFTSDG LHLLTVGTDN RMRLWNSSNG ENTLVNYGKV CNNSKKGLKF TVSCGCSSEF VFVPYGSTIA VYT VYSGEQ ITMLKGHYKT VDCCVFQSNF QELYSGSRDC NILAWVPSLY EPVPDDDETT TKSQLNPAFE DAWSSSDEEG GTSA WSHPQ FEK

UniProtKB: DNA excision repair protein ERCC-8

-
Macromolecule #3: DNA damage-binding protein 1

MacromoleculeName: DNA damage-binding protein 1 / type: protein_or_peptide / ID: 3 / Details: The construct contains an N-terminal His tag. / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 129.298867 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAHHHHHHSA ALEVLFQGPG MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN LLIAKNTRLE IYVVTAEGLR PVKEVGMYGK IAVMELFRP KGESKDLLFI LTAKYNACIL EYKQSGESID IITRAHGNVQ DRIGRPSETG IIGIIDPECR MIGLRLYDGL F KVIPLDRD ...String:
MAHHHHHHSA ALEVLFQGPG MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN LLIAKNTRLE IYVVTAEGLR PVKEVGMYGK IAVMELFRP KGESKDLLFI LTAKYNACIL EYKQSGESID IITRAHGNVQ DRIGRPSETG IIGIIDPECR MIGLRLYDGL F KVIPLDRD NKELKAFNIR LEELHVIDVK FLYGCQAPTI CFVYQDPQGR HVKTYEVSLR EKEFNKGPWK QENVEAEASM VI AVPEPFG GAIIIGQESI TYHNGDKYLA IAPPIIKQST IVCHNRVDPN GSRYLLGDME GRLFMLLLEK EEQMDGTVTL KDL RVELLG ETSIAECLTY LDNGVVFVGS RLGDSQLVKL NVDSNEQGSY VVAMETFTNL GPIVDMCVVD LERQGQGQLV TCSG AFKEG SLRIIRNGIG IHEHASIDLP GIKGLWPLRS DPNRETDDTL VLSFVGQTRV LMLNGEEVEE TELMGFVDDQ QTFFC GNVA HQQLIQITSA SVRLVSQEPK ALVSEWKEPQ AKNISVASCN SSQVVVAVGR ALYYLQIHPQ ELRQISHTEM EHEVAC LDI TPLGDSNGLS PLCAIGLWTD ISARILKLPS FELLHKEMLG GEIIPRSILM TTFESSHYLL CALGDGALFY FGLNIET GL LSDRKKVTLG TQPTVLRTFR SLSTTNVFAC SDRPTVIYSS NHKLVFSNVN LKEVNYMCPL NSDGYPDSLA LANNSTLT I GTIDEIQKLH IRTVPLYESP RKICYQEVSQ CFGVLSSRIE VQDTSGGTTA LRPSASTQAL SSSVSSSKLF SSSTAPHET SFGEEVEVHN LLIIDQHTFE VLHAHQFLQN EYALSLVSCK LGKDPNTYFI VGTAMVYPEE AEPKQGRIVV FQYSDGKLQT VAEKEVKGA VYSMVEFNGK LLASINSTVR LYEWTTEKEL RTECNHYNNI MALYLKTKGD FILVGDLMRS VLLLAYKPME G NFEEIARD FNPNWMSAVE ILDDDNFLGA ENAFNLFVCQ KDSAATTDEE RQHLQEVGLF HLGEFVNVFC HGSLVMQNLG ET STPTQGS VLFGTVNGMI GLVTSLSESW YNLLLDMQNR LNKVIKSVGK IEHSFWRSFH TERKTEPATG FIDGDLIESF LDI SRPKMQ EVVANLQYDD GSGMKREATA DDLIKVVEEL TRIH

UniProtKB: DNA damage-binding protein 1

-
Macromolecule #4: DET1- and DDB1-associated protein 1

MacromoleculeName: DET1- and DDB1-associated protein 1 / type: protein_or_peptide / ID: 4
Details: The construct contains a TwinStrep tag and a Flag tag at the C-terminus.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.997615 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MADFLKGLPV YNKSNFSRFH ADSVCKASNR RPSVYLPTRE YPSEQIIVTE KTNILLRYLH QQWDKKNAAK KRDQEQVELE GESSAPPRK VARTDSPDMH EDTDVLFQGP GAWSHPQFEK GGGSGGGSGG GSWSHPQFEK GASGEDYKDD DDK

UniProtKB: DET1- and DDB1-associated protein 1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.13 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPESHEPES
150.0 mMNaClsodium chloride
0.5 mMTCEPtris(2-carboxyethyl)phosphine
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Details: The grid was coated with graphene oxide.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was glutaraldehyde crosslinked

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
DetailsCollected on Krios 1 at Netherlands Center for Electron Nanoscopy (NeCEN)
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 1382 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 723908
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.3.3)
Details: Combined from focused maps reconstructed with various particle numbers.
Number images used: 294142
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software: (Name: cryoSPARC, RELION (ver. 3.1.3))
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)

-
Atomic model buiding 1

Initial model
PDB IDChainDetails

7oo3

chain_id: P, residue_range: 1-396, source_name: PDB, initial_model_type: experimental modelCSA

7oo3

chain_id: T, residue_range: 1-1140, source_name: PDB, initial_model_type: experimental modelDDB1(BPA/BPC)

6zx9

chain_id: A, residue_range: 393-709, source_name: PDB, initial_model_type: experimental modelDDB1(BPB)

6ud7

chain_id: D, residue_range: 4-76, source_name: PDB, initial_model_type: experimental modelDDA1

yd98

chain_id: A, residue_range: 1-150, source_name: AlphaFold, initial_model_type: in silico modelUVSSA(VHS)
DetailsAdditional densities are observed near several cysteine residues (A/Cys222, A/Cys260, A/Cys288, B/Cys363, B/Cys725, B/Cys1008). We expect these are oxidized products or crosslinking side products.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8qh5:
CryoEM structure of UVSSA(VHS)-CSA-DDB1-DDA1

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more